PD2AF 1.0 Specification
1. Identifying active entities
2. Posttranslational modification (activation and deactivation)
3. Metabolic reactions
4. Empty set (production, degradation, transcription, translation)
5. Heterocomplex association and dissociation
6. Multimerisation
7. Translocation and transport
8. Hidden inhibition
This page offers the specification of the conversion rules. That includes identification of active entities and the translation of Process Description (PD) expressions to Activity Flow (AF) expressions. For each case we ensured that the converter translates exactly as shown: each left-hand diagram (PD) transforms into the corresponding right-hand diagram (AF).
Letter code used for human-readable rule identifiers:
A - active;
AS - association;
AE - active entity;
CURM - currency metabolites;
CAT - catalysis;
CATR - catalysis, reversible process;
COMPL - complex;
CONS - consumption;
DEGR - degradation;
DIS - dissociation;
HIDINH - hidden inhibition;
I - incactive;
INH - inhibition;
INHR - inhibition, reverisible process;
LO - logical operator;
M - metabolite;
MOD - modulation;
MULT - multimerisation;
N - named;
NCURM - noncurrency metabolites;
NSTI - necessery stimulation;
SS - empty set (source/sink);
STI - stimulation;
TRANS - transport;
TRSCR - transcription;
TRSL - tranaslation.
Light green used to highlight active entities.
1. Identifying active entities
The following rules are used for identifying active entities in the context of Process Description maps. Then, in other rules, the status of the entities active vs. inactive is used for adequate conversion. An entity is identified as active if it is marked as “active” in a state variable, or has an outgoing regulatory arc (modulation, stimulation, catalysis, inhibition, necessery stimiulation), or has a consumption arc, or has a logic arc (input to a logical operator).
In graphical visualisatin of these rules we use unspecified entity to show that different types of entities can be in its place such as macromolecule (protein), simple chemical (metabolite), nucleic acid feature (gene, mRNA) or complex.
1.1 PD2AF:AE-A
1.2 PD2AF:AE-MOD
1.3 PD2AF:AE-STI
1.4 PD2AF:AE-CAT
1.5 PD2AF:AE-INH
1.6 PD2AF:AE-NSTI
1.7 PD2AF:AE-LO (NEW)
2. Posttranslational modification (activation and deactivation)
Associated terms: SBO:0000182 conversion, GO:0036211 protein modification process, GO:0140096 catalytic activity, acting on a protein
2.1 PD2AF:I-STI-I
2.2 PD2AF:I-CAT-I
2.3 PD2AF:I-NSTI-I
2.4 PD2AF:I-MOD-I
2.5 PD2AF:I-INH-I
2.6 PD2AF:I-STI-A
2.7 PD2AF:I-CAT-A
2.8 PD2AF:I-NSTI-A
WARNING: Rare or wrong representation of a signalling event.
2.9 PD2AF:I-MOD-A
2.10 PD2AF:I-INH-A
2.11 PD2AF:A-STI-I
2.12 PD2AF:A-CAT-I
2.13 PD2AF:A-NSTI-I
WARNING: Rare or wrong representation of a signalling event.
2.14 PD2AF:A-MOD-I
2.15 PD2AF:A-INH-I
2.16 PD2AF:A-STI-A
2.17 PD2AF:A-CAT-A
2.18 PD2AF:A-NSTI-A
WARNING: Rare or wrong representation of a signalling event.
2.19 PD2AF:A-MOD-A
2.20 PD2AF:A-INH-A
2.21 PD2AF:CURM Currency metabolites
2.22 PD2AF:NCURM Noncurrency metabolites
COMMENT: Modified represetnation in Activity Flow: demerging arcs from the logical operator (not available in the current version of the SBGN standard).
2.23 PD2AF:A-CATR-A
WARNING: Rare or wrong representation of a signalling event.
2.24 PD2AF:I-CATR-A
WARNING: Rare or wrong representation of a signalling event.
2.25 PD2AF:I-INHR-A (AF OUTPUT CORRECTED)
WARNING: Rare or wrong representation of a signalling event.
Associated terms: GO:0008152 metabolic process
3.1 PD2AF:M-CAT-M
3.2 PD2AF:M-STI-M
3.3 PD2AF:M-NSTI-M
WARNING: Rare or wrong representation of a metabolic event.
3.4 PD2AF:M-MOD-M
WARNING: Rare or wrong representation of a metabolic event.
3.5 PD2AF:M-INH-M (AF OUTPUT CORRECTED)
3.6 PD2AF:M-CATR-M
3.7 PD2AF:M-INHR-M (AF OUTPUT CORRECTED)
4. Empty set (production, degradation, transcription, translation)
This section describes processes with an empty set (source/sink) that represents an external pool of entities and is used when we do not need or wish or have enough information to represent specific entities. For example, for the production of a protein, we do not represent all the amino acids and other metabolites used.
Associated terms: SBO:0000179 degradation
4.1 PD2AF:SS-STI
4.2 PD2AF:I-STI-SS
4.3 PD2AF:A-CAT-SS
4.4 PD2AF:A-INH-SS
4.5 PD2AF:SS-TRSCR Trancscription (NEW)
4.6 PD2AF:SS-TRSL Translation (NEW)
5. Heterocomplex association and dissociation
Associated terms: SBO:0000177 non-covalent binding, SBO:0000180 dissociation, GO:0005488 binding
5.1 PD2AF:COMPL-AS-N Heterocomplex association (named complex)
5.2 PD2AF:COMPL-AS Heterocomplex association (unnamed complex)
5.3 PD2AF:COMPL-AS-CAT
5.4 PD2AF:COMPL-DIS
6. Multimerisation
| X = 2; Y = dimer |
X = 7; Y = heptamer |
X = 12; Y = dodecamer |
X = 17; Y = heptadecamer |
| X = 3; Y = trimer |
X = 8; Y = octamer |
X = 13; Y = tridecamer |
X = 18; Y = octadecamer |
| X = 4; Y = tetramer |
X = 9; Y = nonamer |
X = 14; Y = tetradecamer |
X = 19; Y = nonadecamer |
| X = 5; Y = pentamer |
X = 10; Y = decamer |
X = 15; Y = pentadecamer |
X = 20; Y = eicosamer |
| X = 6; Y = hexamer |
X = 11; Y = undecamer |
X = 16; Y = hexadecamer |
X = 21; Y = 21-mer |
6.1 PD2AF:MULT Multimerisation
6.2 PD2AF:MULT-STI Multimerisation regulated
7. Translocation and transport
Associated terms: SBO:0000185 tranlocation reaction, SBO:0000655 transport reaction, GO:0006810 transport
7.1 PD2AF:TRANS
7.1 PD2AF:TRANS-STI
8. Hidden inhibition
8.1 PD2AF:HIDINH1
8.2 PD2AF:HIDINH2
This is a combination of rules 8.1 and 2.7
